Documentation

NDB file format

The NDB format stores 3D genome structures, chromatin annotations, genomic coordinates, and optional interaction records in a plain-text representation. A related binary format, .cndb, is used for compact trajectory data.

Format overview

Each record uses fixed-width fields. The example below highlights the main columns in a .ndb file so coordinates, genomic positions, and annotations are easier to read.

Conversion scripts for .cndb and .ndb files to .pdb, .gro, and .spw are available from the NDB-Converters repository. Additional field-level documentation is available in the NDB documentation notes.

Annotated example

HEADER            NDB File Format Example                      Dec-19
TITLE             The Nucleome Data Bank: Web-based Resources
TITLE             2 Simulate and Analyze the Three-Dimensional Genome
EXPDTA            Simulation - MEGABASE - MiChroM
AUTHOR            Contessoto et. al. - 2019
CYCLE             INTERPHASE     G2
SEQCHR    1  1P     5  A2 B1 B3 A1 B4
SEQCHR    1  1M     5  B2 B3 A1 B3 B1
MODEL     0
CHROM           1 A2  ctcf+   1P          1    0.372   -0.929    0.394            1       50000    1.000
CHROM           2 B1          1P          2    0.410   -0.117    0.953        50001      100000    1.000
CHROM           3 B3          1P          3    0.318    0.857    0.866       100001      150000    1.000
CHROM           4 A1  ctcf-   1P          4    0.321   -0.939    0.272       150001      200000    1.000
CHROM           5 B4          1P          5    1.193    0.923   -0.776       200001      250000    1.000
DNAELE         11 TF           2          1   -1.409   -0.888   -0.631       150001      150500    0.100
...
LOOPS  1     4     COHESIN
LOOPS  5     6     POLYCOMB
END

Field legend

1Nucleome element type

2Index

3Compartment or DNA element

4DNA properties

5Chain identifier

6Index within chain

7X-coordinate

8Y-coordinate

9Z-coordinate

10Genomic position start

11Genomic position end

12Variance of DNA distribution